scholarly journals Thermal Deactivation of Pd/CeO2–ZrO2 Three-Way Catalysts during Real Engine Aging: Analysis by a Surface plus Peripheral Site Model

ACS Omega ◽  
2020 ◽  
Vol 5 (44) ◽  
pp. 28897-28906
Author(s):  
Ayumi Fujiwara ◽  
Yutaro Tsurunari ◽  
Hiroshi Yoshida ◽  
Junya Ohyama ◽  
Tatsuya Yamada ◽  
...  
Keyword(s):  
Thermal Deactivation ◽  
Site Model ◽  
Peripheral Site

Case Report: Hemoptysis localization – hearing with your eyes

POCUS Journal ◽  
2016 ◽  
Vol 1 (2) ◽  
pp. 7
Author(s):  
Barry Chan, MD
Keyword(s):  
Case Report ◽  
Respiratory Failure ◽  
Hemodynamic Instability ◽  
Clinical Vignette ◽  
Massive Hemoptysis ◽  
Airway Patency ◽  
Peripheral Site ◽  
Adventitious Sound

Clinical Vignette: 45 year old was transferred from a peripheral facility for acute massive hemoptysis though maintained sufficient airway patency with no evidence of hemodynamic instability or respiratory failure. Thoracic auscultation revealed vesicular breathing with no adventitious sound. CXR from the peripheral site was normal.

A Phenotype–Genotype Codon Model for Detecting Adaptive Evolution

2019 ◽  
Vol 69 (4) ◽  
pp. 722-738 ◽  
Author(s):  
Christopher T Jones ◽  
Noor Youssef ◽  
Edward Susko ◽  
Joseph P Bielawski
Keyword(s):  
Positive Selection ◽  
Adaptive Evolution ◽  
Evolutionary History ◽  
Life History Trait ◽  
Molecular Adaptation ◽  
Simulation Studies ◽  
Site Model ◽  
Branch Site ◽  
A Site ◽  
Post Hoc

Abstract A central objective in biology is to link adaptive evolution in a gene to structural and/or functional phenotypic novelties. Yet most analytic methods make inferences mainly from either phenotypic data or genetic data alone. A small number of models have been developed to infer correlations between the rate of molecular evolution and changes in a discrete or continuous life history trait. But such correlations are not necessarily evidence of adaptation. Here, we present a novel approach called the phenotype–genotype branch-site model (PG-BSM) designed to detect evidence of adaptive codon evolution associated with discrete-state phenotype evolution. An episode of adaptation is inferred under standard codon substitution models when there is evidence of positive selection in the form of an elevation in the nonsynonymous-to-synonymous rate ratio $\omega$ to a value $\omega > 1$. As it is becoming increasingly clear that $\omega > 1$ can occur without adaptation, the PG-BSM was formulated to infer an instance of adaptive evolution without appealing to evidence of positive selection. The null model makes use of a covarion-like component to account for general heterotachy (i.e., random changes in the evolutionary rate at a site over time). The alternative model employs samples of the phenotypic evolutionary history to test for phenomenological patterns of heterotachy consistent with specific mechanisms of molecular adaptation. These include 1) a persistent increase/decrease in $\omega$ at a site following a change in phenotype (the pattern) consistent with an increase/decrease in the functional importance of the site (the mechanism); and 2) a transient increase in $\omega$ at a site along a branch over which the phenotype changed (the pattern) consistent with a change in the site’s optimal amino acid (the mechanism). Rejection of the null is followed by post hoc analyses to identify sites with strongest evidence for adaptation in association with changes in the phenotype as well as the most likely evolutionary history of the phenotype. Simulation studies based on a novel method for generating mechanistically realistic signatures of molecular adaptation show that the PG-BSM has good statistical properties. Analyses of real alignments show that site patterns identified post hoc are consistent with the specific mechanisms of adaptation included in the alternate model. Further simulation studies show that the covarion-like component of the PG-BSM plays a crucial role in mitigating recently discovered statistical pathologies associated with confounding by accounting for heterotachy-by-any-cause. [Adaptive evolution; branch-site model; confounding; mutation-selection; phenotype–genotype.]

Effects of viscosity and osmotic stress on the reaction of human butyrylcholinesterase with cresyl saligenin phosphate, a toxicant related to aerotoxic syndrome: kinetic and molecular dynamics studies

2013 ◽  
Vol 454 (3) ◽  
pp. 387-399 ◽  
Author(s):  
Patrick Masson ◽  
Sofya Lushchekina ◽  
Lawrence M. Schopfer ◽  
Oksana Lockridge
Keyword(s):  
Osmotic Stress ◽  
Osmotic Pressure ◽  
Active Site ◽  
Md Simulations ◽  
Catalytic Triad ◽  
Wild Type ◽  
Irreversible Inhibitor ◽  
Enzyme Active Site ◽  
Diffusion Controlled ◽  
Peripheral Site

CSP (cresyl saligenin phosphate) is an irreversible inhibitor of human BChE (butyrylcholinesterase) that has been involved in the aerotoxic syndrome. Inhibition under pseudo-first-order conditions is biphasic, reflecting a slow equilibrium between two enzyme states E and E′. The elementary constants for CSP inhibition of wild-type BChE and D70G mutant were determined by studying the dependence of inhibition kinetics on viscosity and osmotic pressure. Glycerol and sucrose were used as viscosogens. Phosphorylation by CSP is sensitive to viscosity and is thus strongly diffusion-controlled (kon≈108 M−1·min−1). Bimolecular rate constants (ki) are about equal to kon values, making CSP one of the fastest inhibitors of BChE. Sucrose caused osmotic stress because it is excluded from the active-site gorge. This depleted the active-site gorge of water. Osmotic activation volumes, determined from the dependence of ki on osmotic pressure, showed that water in the gorge of the D70G mutant is more easily depleted than that in wild-type BChE. This demonstrates the importance of the peripheral site residue Asp70 in controlling the active-site gorge hydration. MD simulations provided new evidence for differences in the motion of water within the gorge of wild-type and D70G enzymes. The effect of viscosogens/osmolytes provided information on the slow equilibrium E⇌E′, indicating that alteration in hydration of a key catalytic residue shifts the equilibrium towards E′. MD simulations showed that glycerol molecules that substitute for water molecules in the enzyme active-site gorge induce a conformational change in the catalytic triad residue His438, leading to the less reactive form E′.

Structural and Spectroscopic Features of acis(Hydroxo)-FeIII-(Carboxylato) Configuration as an Active Site Model for Lipoxygenases

2002 ◽  
Vol 41 (21) ◽  
pp. 5513-5520 ◽  
Author(s):  
Seiji Ogo ◽  
Ryo Yamahara ◽  
Mark Roach ◽  
Tomoyoshi Suenobu ◽  
Michihiko Aki ◽  
...  
Keyword(s):  
Active Site ◽  
Site Model ◽  
Active Site Model

Hydrogenolysis of Ethane on RH Powder. Application of the Landing Site Model

2010 ◽  
Vol 98 (1) ◽  
pp. 49-62 ◽  
Author(s):  
A. Crucq ◽  
L. Degols ◽  
A. Frennet ◽  
G. Lienard
Keyword(s):  
Landing Site ◽  
Site Model

scholarly journals Unbinding of Hyaluronan Accelerates the Enzymatic Activity of Bee Hyaluronidase

2011 ◽  
Vol 286 (41) ◽  
pp. 35699-35707 ◽  
Author(s):  
Attila Iliás ◽  
Károly Liliom ◽  
Brigitte Greiderer-Kleinlercher ◽  
Stephan Reitinger ◽  
Günter Lepperdinger
Keyword(s):  
Experimental Data ◽  
Quartz Crystal ◽  
Surface Loop ◽  
X Ray ◽  
Site Model ◽  
Substrate Interaction ◽  
Close Proximity ◽  
Binding Groove ◽  
The One ◽  
Best Fit

Hyaluronan (HA), a polymeric glycosaminoglycan ubiquitously present in higher animals, is hydrolyzed by hyaluronidases (HAases). Here, we used bee HAase as a model enzyme to study the HA-HAase interaction. Located in close proximity to the active center, a bulky surface loop, which appears to obstruct one end of the substrate binding groove, was found to be functionally involved in HA turnover. To better understand kinetic changes in substrate interaction, binding of high molecular weight HA to catalytically inactive HAase was monitored by means of quartz crystal microbalance technology. Replacement of the delimiting loop by a tetrapeptide interconnection increased the affinity for HA up to 100-fold, with a KD below 1 nm being the highest affinity among HA-binding proteins surveyed so far. The experimental data of HA-HAase interaction were further validated showing best fit to the theoretically proposed sequential two-site model. Besides the one, which had been shown previously in course of x-ray structure determination, a previously unrecognized binding site works in conjunction with an unbinding loop that facilitates liberation of hydrolyzed HA.

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